Hi,
I think your PMF is asymetric because your peptide is asymetric and you
don't sample enough. To get a symetric PMF, your peptide would have to
sample all the possible conformations *and* orientations in each window.
Thus it means that for the windows in the center of the bilayer (where
you say it's extended and interacts with the two monolayers) it'll have
to rotate completely the other way round. This event will probably be
*very* rare because you have to translocate positive charges across the
membrane which cost ~ 40 to 50 kJ/mol (see the PMF of Lys+ and Arg+ in
10.1021/ct700324x).
So as suggested by Chris, Justin and Xavier, you'll have to sample way
more than 100 ns per window. I think you should go at least to the
microsecond time scale (or more?). Or maybe starting from different
initial conformations/orientations for a given window and then
concatenate the different trajectories?
Also consider the remark of Xavier, TM or interfacial peptides are most
of the time alpha-helical within the membrane. So far in literature,
PMFs of a whole peptide across a bilayer were done by restraining the
peptide in a helical conformation (e.g. 10.1016/j.bpj.2010.12.3682). It
is anyway a very difficult problem (and probably impossible at atomistic
resolution) to get a converged PMF for a whole peptide (e.g.
10.1016/j.bpj.2009.03.059).
Ciao,
Patrick
Le 23/02/2011 05:25, Jianguo Li a écrit :
Sorry, why do you think the PMF should be asymmetric?
I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the
membrane) and I did windowed umbrella sampling in the range of d=-1.05nm
to d=9nm. At least the PMF should be symmetric with respect of the
bilayer center in the range of d=[-1.05nm 1.05nm], something like a
guassian distribution. But I got asymmetric PMF in this region. I also
did reverse pulling starting from the peptide below the membrane ending
with the peptide above the membrane. And the subsequent PMF of reversed
pulling is also asymmetic.
I have position restrains of the phosphate beads of the lipids in
z-direction. So the membrane should be stable in REMD. But as you
mentioned, if peptide is truly "stuck" in this orientation, REMD may be
not useful. I will do a single simulation first at a higher temperature
(e.g., 400K) in those bad windows to see if the peptide conformations
are fully sampled.
Cheers,
Jianguo
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Gromacs Users' List <gmx-users@gromacs.org>
*Sent:* Wednesday, 23 February 2011 10:24:46
*Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
Jianguo Li wrote:
> Thank you, Justin.
> Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm.
Since I think there is no problem in the region out of the membrane, so
I only show the configurations within the membrane. My objective is to
access the free energy barrier of the peptide translocate the negatively
charged membrane. The problem is that the PMF is not symmetric with
respect to the bilayer center due to the unconverged simulations.
I would argue that the PMF is not symmetric because your reaction
coordinate is not symmetric. How can you calculate a free energy of
crossing a charged membrane when your peptide does not cross the
membrane? What I proposed earlier was to obtain configurations at equal
distances "above" and "below" the membrane (arbitrary in a periodic
system, but hopefully you get the idea). If you can extract the peptide
to the point where it is liberated from the membrane in the negative
direction, I'd suspect you could solve your problem.
> Since g_wham does not support different temperatures in different
windows, to increase the converges, I will probably consider to do REMD
in those bad windows.
>
This technique might work, provided you don't destabilize the membrane,
but if the peptide is truly "stuck" in this orientation, I doubt that
limited-range REMD would be very useful.
-Justin
> Cheers
> Jianguo
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Gromacs Users' List <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> *Sent:* Tuesday, 22 February 2011 21:10:08
> *Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
>
>
>
> Jianguo Li wrote:
> > Thanks Justin and Chris and sorry for confusing interpretation.
> > Let me make it more clear. My peptide is flexible Martini beads,
and highly positively charged. My membrane is a mixture of negatively
charged lipids (25%) and zitterionic lipids(75%). So there is strong
electrostatic attraction
> > between peptide and membrane. To get the PMF, I did the following:
> >
> > (1) I did pulling simulation along (0 0 -1) direction to pull my
peptide across the membrane. Then I got different configurations
corresponding to different windows along the reaction coordinates, which
is the z-distance
> > between peptide and membrane. This figure
(http://www.flickr.com/photos/lijg/5467080971/) shows some of the
configurations at certain reaction coordinates.
> >
>
> Are you not sampling configurations outside of the membrane (i.e. in
water)? I would think that would solve your problem. You don't show any
configurations in which the peptide is completely dissociated from the
membrane. I don't know your objectives, but I would think that if you
could completely extract the peptide from the membrane after passing
through it, this would solve your problem.
>
> > (2) In each window, I used the corresponding configuration that
generated by the pulling simulation as initial input and run umbrella
sampling. The size of each window is 0.15 nm, but close to the bilayer
cneter (e.g., -0.6<d<0.6), I have
> > increased number of windows so that the width of the window is to
be 0.05 or 0.1 nm, I also tried to use different force constant in these
windows.
> >
> > From the figure (http://www.flickr.com/photos/lijg/5467080971/) ,
we can classify the peptide conformation to be either extended
(interacting with two bilayers) or compact (interacting with only one
bilayer). Ideally, the peptide conformation should be similar for d=x
and d=-x. The problem is that the configuration of peptide is not
symmetric with respect to the bilayer center. For example, the peptide
configuration is compact at d=0.6 and d=0.9, but the peptide is extended
at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate
PMF, then the PMF is not symmetric with respect to the bilayer center.
Using more number of windows and different force constant did not remove
the problem.
> >
> > In my opinion, at least in some windows, the peptide should sample
both compact and extended structure. But what I found is that the windowed
>
> Don't pre-judge the model :) Also, as I said before, there is no
reason to suspect that MARTINI will produce any meaningful secondary
structure changes. It was not parameterized to do so.
>
> > umbrella simulation depends on the initial peptide conformation. If
the initial peptide conformation is compact, then after 100 ns, it is
still compact; if the initial peptide in that window is extended, the
final configuration is also extended. I also tried to run longer
equilibrium time (e.g., 200 ns), but the problem still exists.
> >
>
> Sounds like a limitation of the force field model.
>
> > My question is how to increase sampling of the peptide
conformation? I just think of two choices:
> > (1) use high temperature (e.g., 500K) at those bad windows. As I
mentioned, I am wondering if g_wham can unbias the effect of using
different temperatures in different windows.
> > (2) use REMD in those bad windows. These need a lot of
computational resources.
> >
>
> Neither of these will be useful in generating a sensible PMF curve.
WHAM needs a single temperature for proper weighting. If you start
including different temperatures in different regions of phase space, I
would imagine the weighting would be completely incorrect.
>
> Note that SMD is not the only option for generating starting
configurations. If you think that certain orientations or configurations
are "correct," you can build them yourself, but keep in mind that you'll
have to justify this procedure to a skeptical audience.
>
> -Justin
>
> > Is there any other method to deal with the insufficient sampling?
> > Any suggestions are welcome, thanks for your time reading this email!
> >
> > Cheers,
> > Jianguo
> >
> >
> >
------------------------------------------------------------------------
> > *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
> > *To:* Gromacs Users' List <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
> > *Sent:* Tuesday, 22 February 2011 11:13:05
> > *Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
>
--
_______________________________________________________________________
!!!! new E-mail address: patrick.fu...@univ-paris-diderot.fr !!!!
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
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